--- title: "Request a previously stored response from the server" method: GET path: "/response/{response_id}" tags: ["response"] --- # Request a previously stored response from the server `GET /response/{response_id}` ## Path parameters - `response_id` string, required ## Response `200` successful operation - Response — The Response object contains the main payload when a TRAPI query endpoint interprets and responds to the submitted query successfully (i.e., HTTP Status Code 200). The message property contains the knowledge of the response (query graph, knowledge graph, and results). The status, description, and logs properties provide additional details about the response. - `message` Message, required — The message object holds the main content of a Query or a Response in three properties: query_graph, results, and knowledge_graph. The query_graph property contains the query configuration, the results property contains any answers that are returned by the service, and knowledge_graph property contains lists of edges and nodes in the thought graph corresponding to this message. The content of these properties is context-dependent to the encompassing object and the TRAPI operation requested. - `results` Result[], nullable — List of all returned Result objects for the query posed. The list SHOULD NOT be assumed to be ordered. The 'score' property, if present, MAY be used to infer result rankings. If Results are not expected (such as for a query Message), this property SHOULD be null or absent. If Results are expected (such as for a response Message) and no Results are available, this property SHOULD be an array with 0 Results in it. - `node_bindings` object, required — The dictionary of Input Query Graph to Result Knowledge Graph node bindings where the dictionary keys are the key identifiers of the Query Graph nodes and the associated values of those keys are instances of NodeBinding schema type (see below). This value is an array of NodeBindings since a given query node may have multiple knowledge graph Node bindings in the result. - `analyses` Analysis[], required — The list of all Analysis components that contribute to the result. See below for Analysis components. - `resource_id` string, required — A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI. - `score` number, float, nullable — A numerical score associated with this result indicating the relevance or confidence of this result relative to others in the returned set. Higher MUST be better. - `edge_bindings` object, required — The dictionary of input Query Graph to Knowledge Graph edge bindings where the dictionary keys are the key identifiers of the Query Graph edges and the associated values of those keys are instances of EdgeBinding schema type (see below). This value is an array of EdgeBindings since a given query edge may resolve to multiple Knowledge Graph Edges. - `support_graphs` string[], nullable — This is a list of references to Auxiliary Graph instances that supported the analysis of a Result as performed by the reasoning service. Each item in the list is the key of a single Auxiliary Graph. - `scoring_method` string, nullable — An identifier and link to an explanation for the method used to generate the score - `attributes` Attribute[], nullable — The attributes of this particular Analysis. - `attribute_type_id` string, required — A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI. - `original_attribute_name` string, nullable — The term used by the original source of an attribute to describe the meaning or significance of the value it captures. This may be a column name in a source tsv file, or a key in a source json document for the field in the data that held the attribute's value. Capturing this information where possible lets us preserve what the original source said. Note that the data type is string' but the contents of the field could also be a CURIE of a third party ontology term. - `value` unknown, required - `value_type_id` string — A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI. - `attribute_source` string, nullable — The source of the core assertion made by the key-value pair of an attribute object. Use a CURIE or namespace designator for this resource where possible. - `value_url` string, nullable — Human-consumable URL linking to a web document that provides additional information about an attribute's value (not the node or the edge fom which it hangs). - `description` string, nullable — Human-readable description for the attribute and its value. - `attributes` Attribute[], nullable — A list of attributes providing further information about the parent attribute (for example to provide provenance information about the parent attribute). - `id` string, nullable — URI for this result - `description` string, nullable — A free text description of this result answer from the reasoner - `essence` string, nullable — A single string that is the terse essence of the result (useful for simple answers) - `essence_category` string, nullable — A Translator BioLink bioentity category of the essence - `row_data` union[], nullable — An arbitrary list of values that captures the essence of the result that can be turned into a tabular result across all answers (each result is a row) for a user that wants simplified tabular output - union - string - number - `score` number, float, nullable — A numerical score associated with this result indicating the relevance or confidence of this result relative to others in the returned set. Higher MUST be better. - `score_name` string, nullable — Name for the score - `score_direction` string, nullable — Sorting indicator for the score: one of higher_is_better or lower_is_better - `confidence` number, float, nullable — Confidence metric for this result, a value between (inclusive) 0.0 (no confidence) and 1.0 (highest confidence) - `result_group` integer, nullable — An integer group number for results for use in cases where several results should be grouped together. Also useful to control sorting ascending. - `result_group_similarity_score` number, float, nullable — A score that denotes the similarity of this result to other members of the result_group - `resource_id` string, nullable — Identifier string of the resource that provided this result (one of ARAX, Aragorn, etc.) - `query_graph` QueryGraph — A graph representing a biomedical question. It serves as a template for each result (answer), where each bound knowledge graph node/edge is expected to obey the constraints of the associated query graph element. - `nodes` object, required — The node specifications. The keys of this map are unique node identifiers and the corresponding values include the constraints on bound nodes. - `edges` object, required — The edge specifications. The keys of this map are unique edge identifiers and the corresponding values include the constraints on bound edges, in addition to specifying the subject and object QNodes. - `knowledge_graph` KnowledgeGraph — The knowledge graph associated with a set of results. The instances of Node and Edge defining this graph represent instances of biolink:NamedThing (concept nodes) and biolink:Association (relationship edges) representing (Attribute) annotated knowledge returned from the knowledge sources and inference agents wrapped by the given TRAPI implementation. - `nodes` object, required — Dictionary of Node instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key. - `edges` object, required — Dictionary of Edge instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key. - `auxiliary_graphs` object — Dictionary of AuxiliaryGraph instances that are used by Knowledge Graph Edges and Result Analyses. These are referenced elsewhere by the dictionary key. - `status` string, nullable — One of a standardized set of short codes, e.g. Success, QueryNotTraversable, KPsNotAvailable - `description` string, nullable — A brief human-readable description of the outcome - `logs` LogEntry[], nullable — A list of LogEntry items, containing errors, warnings, debugging information, etc. List items MUST be in chronological order with earliest first. - `timestamp` string, date-time, required — Timestamp in ISO 8601 format, providing the LogEntry time either in univeral coordinated time (UTC) using the 'Z' tag (e.g 2020-09-03T18:13:49Z), or, if local time is provided, the timezone offset must be provided (e.g. 2020-09-03T18:13:49-04:00). - `level` 'ERROR' | 'WARNING' | 'INFO' | 'DEBUG' — Logging level - `code` string, nullable — One of a standardized set of short codes e.g. QueryNotTraversable, KPNotAvailable, KPResponseMalformed - `message` string, required — A human-readable log message - `workflow` union[] — A list of operations that were executed. - union - OperationAnnotate — This operation adds attributes to knowledge graph elements. - `id` 'annotate', required - `parameters` unknown - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationAnnotateEdges — This operation adds attributes to knowledge graph edges. - `id` 'annotate_edges', required - `parameters` OperationAnnotateEdgesParameters - `attributes` string[] — A list of attributes to annotate the edges with. If not included then all available data will be annotated. - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationAnnotateNodes — This operation adds attributes to knowledge graph nodes. - `id` 'annotate_nodes', required - `parameters` OperationAnnotateNodesParameters - `attributes` string[] — A list of attributes to annotate the nodes with. If not included then all available data will be annotated. - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationBind — This operation adds results binding kgraph elements to qgraph elements. - `id` 'bind', required - `parameters` unknown - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationCompleteResults — This operation combines partial results into complete results. - `id` 'complete_results', required - `parameters` unknown - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationEnrichResults — Create new results by applying enrichment analysis to existing results. In particular, combines results by transforming a qnode into a set, formed of knodes that share a property or relation more often than expected by chance. - `id` 'enrich_results', required - `parameters` OperationEnrichResultsParameters - `pvalue_threshold` number — The cutoff p-value for enrichment. - `qnode_keys` string[] — If specified, then only knodes bound to these qnodes will be examined for enrichment and combination. - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationFill — This operation adds knodes and kedges. Any constraints attached to QNodes and QEdges specified in the TRAPI must be respected. - `id` 'fill', required - `parameters` union - object - `allowlist` string[] — List of knowledge providers/sources that may be used to provide knowledge. - `qedge_keys` string[] — A list of qedge keys. If included only edges corresponding to the given qedge keys, as well as their connected nodes, will be filled. If not included all edges will be filled. - object - `denylist` string[] — List of knowledge providers/sources that may NOT be used to provide knowledge. - `qedge_keys` string[] — A list of qedge keys. If included only edges corresponding to the given qedge keys, as well as their connected nodes, will be filled. If not included all edges will be filled. - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationFilterKgraph — This operation removes kgraph elements (nodes and/or edges). - `id` 'filter_kgraph', required - `parameters` unknown - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationFilterKgraphContinuousKedgeAttribute — This operation removes kgraph edges based on the value of a continuous edge attribute. Edges without the given attribute are left alone. - `id` 'filter_kgraph_continuous_kedge_attribute', required - `parameters` OperationFilterKgraphContinuousKedgeAttributeParameters, required - `edge_attribute` string, required — The name of the edge attribute to filter on. - `qedge_keys` string[] — This indicates if you only want to remove edges with specific edge_keys. If not provided or empty, all edges will be filtered on. - `qnode_keys` string[] — This indicates if you only want nodes corresponding to a specific list of qnode_keys to be removed. If not provided or empty, no nodes will be removed when filtering. Allows us to know what to do with the nodes connected to edges that are removed. - `remove_above_or_below` 'above' | 'below', required — Indicates whether to remove above or below the given threshold. - `threshold` number, required — The value to compare attribute values to. - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationFilterKgraphDiscreteKedgeAttribute — This operation removes kgraph edges which have a discrete attribute containing the specified value. Edges without the given attribute are left alone. - `id` 'filter_kgraph_discrete_kedge_attribute', required - `parameters` OperationFilterKgraphDiscreteKedgeAttributeParameters, required - `edge_attribute` string, required — The name of the edge attribute to filter on. - `qedge_keys` string[] — This indicates if you only want to remove edges with specific edge_keys. If not provided or empty, all edges will be filtered on. - `qnode_keys` string[] — This indicates if you only want nodes corresponding to a specific list of qnode_keys to be removed. If not provided or empty, no nodes will be removed when filtering. Allows us to know what to do with the nodes connected to edges that are removed - `remove_value` string, required — The value for which all edges containing this value in the specified edge_attribute should be removed. - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationFilterKgraphDiscreteKnodeAttribute — This operation removes kgraph nodes which have a discrete attribute containing the specified value. In TRAPI 1.1+ this will look in the `attribute_type_id` and `original_attribute_name` attribute fields for the attribute name. Node without the given attribute are left alone. Edges connecting to the removed nodes will also be removed. - `id` 'filter_kgraph_discrete_knode_attribute', required - `parameters` OperationFilterKgraphDiscreteKnodeAttributeParameters, required - `node_attribute` string, required — The name of the node attribute to filter on. - `qnode_keys` string[] — This indicates if you only want to remove nodes corresponding to a specific list of qnode_keys to be removed. If not provided or empty, all nodes will be considered when filtering. - `remove_value` string, required — The value for which all edges containing this value in the specified edge_attribute should be removed. - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationFilterKgraphOrphans — This operation removes kgraph elements that are not referenced by any results. - `id` 'filter_kgraph_orphans', required - `parameters` unknown - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationFilterKgraphPercentile — This operation removes kgraph edges that have attribute values are below/above the given percentile. - `id` 'filter_kgraph_percentile', required - `parameters` OperationFilterKgraphPercentileParameters, required - `edge_attribute` string, required — The name of the edge attribute to filter on. - `qedge_keys` string[] — This indicates if you only want to filter on specific edge_keys. If not provided or empty, all edges will be filtered on. - `qnode_keys` string[] — This indicates if you only want nodes corresponding to a specific list of qnode_keys to be removed. If not provided or empty, no nodes will be removed when filtering. Allows us to know what to do with the nodes connected to edges that are removed. - `remove_above_or_below` 'above' | 'below' — Indicates whether to remove above or below the given threshold. - `threshold` number — The percentile to threshold on. - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationFilterKgraphStdDev — This operation removes kgraph edges that have attribute values are below/above the mean +/- n standard deviations. - `id` 'filter_kgraph_std_dev', required - `parameters` OperationFilterKgraphStdDevParameters, required - `edge_attribute` string, required — The name of the edge attribute to filter on. - `num_sigma` number — The number of standard deviations to threshold on. - `plus_or_minus_std_dev` 'plus' | 'minus' — Indicate whether or not the threshold should be found using plus or minus the standard deviation. E.g. when plus_or_minus_std_dev is set to plus will set the cutoff for filtering as the mean + num_sigma * std_dev while setting plus_or_minus_std_dev to minus will set the cutoff as the mean - num_sigma * std_dev. - `qedge_keys` string[] — This indicates if you only want to filter on specific edge_keys. If not provided or empty, all edges will be filtered on. - `qnode_keys` string[] — This indicates if you only want nodes corresponding to a specific list of qnode_keys to be removed. If not provided or empty, no nodes will be removed when filtering. - `remove_above_or_below` 'above' | 'below' — Indictes whether to remove above or below the given threshold. - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationFilterKgraphTopN — This operation removes kgraph edges that have attribute values are below/above the top/bottom n values. - `id` 'filter_kgraph_top_n', required - `parameters` OperationFilterKgraphTopNParameters, required - `edge_attribute` string, required — The name of the edge attribute to filter on. - `keep_top_or_bottom` 'top' | 'bottom' — Indicate whether or not the the top or bottom n values should be kept. - `max_edges` integer — The number of edges to keep. - `qedge_keys` string[] — This indicates if you only want to filter on specific edge_keys. If not provided or empty, all edges will be filtered on. - `qnode_keys` string[] — This indicates if you only want nodes corresponding to a specific list of qnode_keys to be removed. If not provided or empty, no nodes will be removed when filtering. Allows us to know what to do with the nodes connected to edges that are removed. - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationFilterResults — This operation allows the TRAPI server to remove elements from the list of results. - `id` 'filter_results', required - `parameters` unknown - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationFilterResultsTopN — This operation truncates the results to at most `max_results` that appear in the TRAPI JSON message. - `id` 'filter_results_top_n', required - `parameters` OperationFilterResultsTopNParameters, required - `max_results` integer, required — The maximum number of results to return. - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationLookup — This operation adds knodes/kedges and (complete) results. It is equivalent to the workflow fill + bind + complete_results. Any constraints attached to QNodes and QEdges specified in the TRAPI must be respected. - `id` 'lookup', required - `parameters` unknown - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationLookupAndScore — This operation adds knodes/kedges, (complete) results, and scores (to the results). It is equivalent to the workflow fill + bind + complete_results + score. Any constraints attached to QNodes and QEdges specified in the TRAPI must be respected. - `id` 'lookup_and_score', required - `parameters` unknown - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationOverlay — This operation adds additional qedges and/or kedges and/or result edge bindings. - `id` 'overlay', required - `parameters` unknown - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationOverlayComputeJaccard — This operation computes the Jaccard Similarity which measures how many intermediate_node_key nodes are directly connected to both the end_node_keys nodes for all pairs of nodes with corresponding keys. It will then add edges to the knowledge graph along with edge attributes (with the property name jaccard_index) between each start_node_key and object_node_key. A query graph edge will also be added using the key specified by virtual_relation_label. This is used for purposes such as "find me all drugs (start_node_key) that have many proteins (intermediate_node_key) in common with this disease (end_node_key)." This can be used for downstream filtering to concentrate on relevant bioentities. - `id` 'overlay_compute_jaccard', required - `parameters` OperationOverlayComputeJaccardParameters, required - `end_node_keys` string[], required — A list of qnode keys specifying the ending nodes. - `intermediate_node_key` string, required — A qnode key specifying the intermediate node. - `virtual_relation_label` string, required — The key of the query graph edge that corresponds to the knowledge graph edges that were added by this operation. - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationOverlayComputeNgd — This operation computes the normalized Google distance (co-occurrence frequency) in PubMed abstracts and adds virual edges between qnodes AND/OR knodes AND/OR results edge bindings. If no publications are found infinity is returned. - `id` 'overlay_compute_ngd', required - `parameters` OperationOverlayComputeNgdParameters, required - `qnode_keys` string[], required — A list of qnode keys to overlay pairwise edges onto. Must be be a list of at least 2 valid qnodes. - `virtual_relation_label` string, required — An label to help identify the virtual edge in the relation field - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationOverlayConnectKnodes — Given a TRAPI message, create new kedges between existing knodes. These may be created using arbitrary methods or data sources, though provenance should be attached to the new kedges. Each new kedge is also added to all results containing node bindings to both the subject and object knodes. This may be independent of any qedge connections, i.e. kedges can be created between any nodes in the kgraph. - `id` 'overlay_connect_knodes', required - `parameters` unknown - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationOverlayFisherExactTest — Fisher exact test computes the Fisher's Exact Test p-values of the connection between a list of given nodes with specified query id (subject_qnode_key e.g. n01) to their adjacent nodes with specified query id (object_qnode_key e.g. n02) in the message knowledge graph. This information is then added as an edge attribute to a virtual edge which is then added to the query graph and knowledge graph. It can also allow you to filter out the user-defined insignificance of connections based on a specified p-value cutoff or return the top n smallest p-value of connections and only add their corresponding virtual edges to the knowledge graph. - `id` 'overlay_fisher_exact_test', required - `parameters` OperationOverlayFisherExactTestParameters, required - `object_qnode_key` string, required — A specific object query node id. - `rel_edge_key` string — A specific Qedge id connected to both subject nodes and object nodes in message KG (optional, otherwise all edges connected to both subject nodes and object nodes in message KG are considered). - `subject_qnode_key` string, required — A specific subject query node id. - `virtual_relation_label` string, required — An label to help identify the virtual edge. - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationRestate — This operation modifies the query graph. - `id` 'restate', required - `parameters` unknown - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationScore — This operation adds scores to results. - `id` 'score', required - `parameters` unknown - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationSortResults — This operation allows the TRAPI server to sort the elements of the list of results. - `id` 'sort_results', required - `parameters` unknown - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationSortResultsEdgeAttribute — This operation sorts the results by the given edge attribute. If in ascending order, the minimum value of the results edges with the given attribute will be taken while the maximum will be taken for descending order. If a result has no edges with the given attribute, it will be listed last. If `max_results` is given, it truncates the results to at most the given value. - `id` 'sort_results_edge_attribute', required - `parameters` OperationSortResultsEdgeAttributeParameters, required - `ascending_or_descending` 'ascending' | 'descending', required — Indicates whether results should be sorted in ascending or descending order. - `edge_attribute` string, required — The name of the edge attribute to order by. - `qedge_keys` string[] — This indicates if you only want to consider edges with specific edge_keys. If not provided or empty, all edges will be looked at. - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationSortResultsNodeAttribute — This operation sorts the results by the given node attribute. If in ascending order, the minimum value of the results nodes with the given attribute will be taken while the maximum will be taken for descending order. If a result has no nodes with the given attribute, it will be listed last. If `max_results` is given, it truncates the results to at most the given value. - `id` 'sort_results_node_attribute', required - `parameters` OperationSortResultsNodeAttributeParameters, required - `ascending_or_descending` 'ascending' | 'descending', required — Indicates whether results should be sorted in ascending or descending order. - `node_attribute` string, required — The name of the node attribute to order by. - `qnode_keys` string[] — This indicates if you only want to consider nodes with specific node_keys. If not provided or empty, all nodes will be looked at. - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - OperationSortResultsScore — This operation sorts the results by the result score. If `max_results` is given, it truncates the results to at most the given value. - `id` 'sort_results_score', required - `parameters` OperationSortResultsScoreParameters, required - `ascending_or_descending` 'ascending' | 'descending', required — Indicates whether results should be sorted in ascending or descending order. - `runner_parameters` union - object - `allowlist` string[] — List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. - object - `denylist` string[] — List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. - `unique` boolean - `submitter` string, nullable — Any string for self-identifying the submitter of a query. The purpose of this optional field is to aid in the tracking of the source of queries for development and issue resolution. - `operations` Operations, nullable — Container for one or more Message objects or identifiers for one or more Messages along with a processing plan and options for how those messages should be processed and returned - `message_uris` string[] — List of URIs for Message or Response objects to fetch and process - `messages` Message[] — List of Message objects to process - `results` Result[], nullable — List of all returned Result objects for the query posed. The list SHOULD NOT be assumed to be ordered. The 'score' property, if present, MAY be used to infer result rankings. If Results are not expected (such as for a query Message), this property SHOULD be null or absent. If Results are expected (such as for a response Message) and no Results are available, this property SHOULD be an array with 0 Results in it. - `node_bindings` object, required — The dictionary of Input Query Graph to Result Knowledge Graph node bindings where the dictionary keys are the key identifiers of the Query Graph nodes and the associated values of those keys are instances of NodeBinding schema type (see below). This value is an array of NodeBindings since a given query node may have multiple knowledge graph Node bindings in the result. - `analyses` Analysis[], required — The list of all Analysis components that contribute to the result. See below for Analysis components. - `resource_id` string, required — A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI. - `score` number, float, nullable — A numerical score associated with this result indicating the relevance or confidence of this result relative to others in the returned set. Higher MUST be better. - `edge_bindings` object, required — The dictionary of input Query Graph to Knowledge Graph edge bindings where the dictionary keys are the key identifiers of the Query Graph edges and the associated values of those keys are instances of EdgeBinding schema type (see below). This value is an array of EdgeBindings since a given query edge may resolve to multiple Knowledge Graph Edges. - `support_graphs` string[], nullable — This is a list of references to Auxiliary Graph instances that supported the analysis of a Result as performed by the reasoning service. Each item in the list is the key of a single Auxiliary Graph. - `scoring_method` string, nullable — An identifier and link to an explanation for the method used to generate the score - `attributes` Attribute[], nullable — The attributes of this particular Analysis. - `attribute_type_id` string, required — A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI. - `original_attribute_name` string, nullable — The term used by the original source of an attribute to describe the meaning or significance of the value it captures. This may be a column name in a source tsv file, or a key in a source json document for the field in the data that held the attribute's value. Capturing this information where possible lets us preserve what the original source said. Note that the data type is string' but the contents of the field could also be a CURIE of a third party ontology term. - `value` unknown, required - `value_type_id` string — A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI. - `attribute_source` string, nullable — The source of the core assertion made by the key-value pair of an attribute object. Use a CURIE or namespace designator for this resource where possible. - `value_url` string, nullable — Human-consumable URL linking to a web document that provides additional information about an attribute's value (not the node or the edge fom which it hangs). - `description` string, nullable — Human-readable description for the attribute and its value. - `attributes` Attribute[], nullable — A list of attributes providing further information about the parent attribute (for example to provide provenance information about the parent attribute). - `id` string, nullable — URI for this result - `description` string, nullable — A free text description of this result answer from the reasoner - `essence` string, nullable — A single string that is the terse essence of the result (useful for simple answers) - `essence_category` string, nullable — A Translator BioLink bioentity category of the essence - `row_data` union[], nullable — An arbitrary list of values that captures the essence of the result that can be turned into a tabular result across all answers (each result is a row) for a user that wants simplified tabular output - union - string - number - `score` number, float, nullable — A numerical score associated with this result indicating the relevance or confidence of this result relative to others in the returned set. Higher MUST be better. - `score_name` string, nullable — Name for the score - `score_direction` string, nullable — Sorting indicator for the score: one of higher_is_better or lower_is_better - `confidence` number, float, nullable — Confidence metric for this result, a value between (inclusive) 0.0 (no confidence) and 1.0 (highest confidence) - `result_group` integer, nullable — An integer group number for results for use in cases where several results should be grouped together. Also useful to control sorting ascending. - `result_group_similarity_score` number, float, nullable — A score that denotes the similarity of this result to other members of the result_group - `resource_id` string, nullable — Identifier string of the resource that provided this result (one of ARAX, Aragorn, etc.) - `query_graph` QueryGraph — A graph representing a biomedical question. It serves as a template for each result (answer), where each bound knowledge graph node/edge is expected to obey the constraints of the associated query graph element. - `nodes` object, required — The node specifications. The keys of this map are unique node identifiers and the corresponding values include the constraints on bound nodes. - `edges` object, required — The edge specifications. The keys of this map are unique edge identifiers and the corresponding values include the constraints on bound edges, in addition to specifying the subject and object QNodes. - `knowledge_graph` KnowledgeGraph — The knowledge graph associated with a set of results. The instances of Node and Edge defining this graph represent instances of biolink:NamedThing (concept nodes) and biolink:Association (relationship edges) representing (Attribute) annotated knowledge returned from the knowledge sources and inference agents wrapped by the given TRAPI implementation. - `nodes` object, required — Dictionary of Node instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key. - `edges` object, required — Dictionary of Edge instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key. - `auxiliary_graphs` object — Dictionary of AuxiliaryGraph instances that are used by Knowledge Graph Edges and Result Analyses. These are referenced elsewhere by the dictionary key. - `actions` string[] — List of order-dependent operations to execute - `options` object — Map of order independent options that apply during processing - `job_id` string, nullable — An identifier for the submitted job that can be used with /async_query_status to receive an update on the status of the job. - `resource_id` string, nullable — Identifier string of the resource that provided this response (one of ARAX, Aragorn, etc.) - `tool_version` string — Version label of the tool that generated this response - `schema_version` string — Version label of this TRAPI schema - `biolink_version` string — Version label of the Biolink model used in this document - `datetime` string — Datetime string for the time that this response was generated - `table_column_names` string[] — List of column names that corresponds to the row_data for each result - `original_question` string — The original question text typed in by the user - `restated_question` string — A precise restatement of the question, as understood by the Translator, for which the answer applies. The user should verify that the restated question matches the intent of their original question (it might not). - `query_options` object — Dict of options that can be sent with the query. Options are tool specific and not stipulated here - `context` string — JSON-LD context URI - `type` string — Entity type of this response - `id` string — URI for this response - `validation_result` object — Validation results and other summary stats computed for this Response. - `total_results_count` integer, nullable — The total number of results that were generated prior to any filtering. - `info` string, nullable — A placholder for including some additional information ## Other responses - `404` — response_id not found --- [API](https://skmtc.net/rtxteam/apis/arax-translator-reasoner-trapi-1-6-0.md) · [All operations](https://skmtc.net/rtxteam/apis/arax-translator-reasoner-trapi-1-6-0/llms.txt) · [OpenAPI document](https://skmtc-service-staging.skmtc.workers.dev/v1/apis/rtxteam/arax-translator-reasoner-trapi-1-6-0/revisions/d34f07f69837/schema)